Images cliquables

Clicking on the html file (generated by biojs)


  • Warning: use the horizontal scrollbar of the window + the right click of the mouse on the alignment to see the left part of the representation.

  • To change the aligments colors (“Nucleotide” recommanded for nucleotides):



  • To annotate the FR and CDR regions, use the biojs.gff file in the same folder than the opened .html file:



  • Schematic illustration of these regions:



  • Export as picture does not work well as part of the sequence not displayed are not exported (screenshot). Use Jalview, as explained below.






Jalview


In Jalview:
  • Drag and drop the .fasta file with the same name as the .html file (in the alignment folder), or use the menu file:



  • To stain nuc or aa letters:
    • Add colors:



    • Set a threshold to see the differences:



    • A high threshold set all the columns with at least one difference in white:



    • A low threshold set all the different minority events in each column in white:



  • To add features:
    • Drag and drop a jalview.gff file on the sequence, or use the menu file:



    • To change the feature colors:



    • To reset the features:



  • To export as .png for instance:





Abalign


In Abalign, import a fasta file from the alignment folder and analyze interactively.

Warning: if the align_seq parameter of the nextflow.config file is query, then the vizualization is performed only for the aa sequences that are in phase (i.e., that have identifiable v, d or j regions).